tag:blogger.com,1999:blog-7785493.post691928398852094946..comments2017-08-16T10:03:44.552+03:00Comments on Dienekes’ Anthropology Blog: Clusters Galore (fastIBD edition)Dienekeshttp://www.blogger.com/profile/02082684850093948970noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-7785493.post-45719913133334491032012-04-06T13:08:44.850+03:002012-04-06T13:08:44.850+03:00@Qinsi
fastIBD outputs a file ending in
*.fibd....@Qinsi<br /><br />fastIBD outputs a file ending in <br /><br />*.fibd.gz<br /><br />This file contains shared segments between individuals. Gunzip it, and you&#39;ll see that each line has five elements:<br /><br />IDs of the two individuals<br />beginning and end marker index<br />probability<br /><br />This is explained in the Beagle manual.<br /><br />What you need to do is for each line to calculate the length of the segment by substracting the genetic positions (in bp): end-beginning. If there is a recombination map for whatever species you are dealing with, then you can do the subtraction in cM instead.<br /><br />You then have an NxN matrix which you initialize with 0, and whenever the i-th individual shares a segment with the j-th individual, you add the length of the segment to the (i, j) entry. In the end, you get a matrix of sharing between different individuals. If you subtract this from its maximum value, then you get a matrix of not-sharing, which can be used as a distance matrix.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-90913614566173992282012-04-06T11:17:33.830+03:002012-04-06T11:17:33.830+03:00Hi，I&#39;m a new to this area.
I want get the pop...Hi，I&#39;m a new to this area. <br />I want get the population structrue of Soybean by FastIBD(Beagle). Now I have fastIBD results how do I get the matrix from “The end result of my labors is an NxN matrix”.Qinsihttps://www.blogger.com/profile/03670646176345767415noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-53072209298728100622012-01-21T11:52:03.600+02:002012-01-21T11:52:03.600+02:00That surely corroborates the traditional historica...<i>That surely corroborates the traditional historical account that the English are descended from &quot;Anglo-Saxon&quot; west Germanic tribes who migrated from Angeln and Lower Saxony in Germany and from Jutland (Denmark) to England via -- and who also settled -- the Frisian coastal regions of Holland and Germany.</i><br /><br />I maintain that this connection - in addition to what you mention - also goes farther back in time.<br /><br />(i) The agriculturalists who entered the Isles likely were identical to those settling along the &quot;North Sea,&quot; in the first place (but different from the &quot;natives&quot; - who likely were were <i>majority</i> southwestern after the Younger Dryas, rather than northeastern like much of the central/northeastern continent.<br /><br />(ii) There is evidence from the historical record as well as from excavated typical Germanic houses that there were Germanic settlements during, and perhaps even before Roman times along England&#39;s east coast. Which is not surprising, given generally strong and peaceful trade in the region for many centuries, if not more than a millennium.eurologisthttps://www.blogger.com/profile/03440019181278830033noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-37947528196455480032012-01-14T19:27:47.350+02:002012-01-14T19:27:47.350+02:00That surely corroborates the traditional historica...<i>That surely corroborates the traditional historical account that the English are descended from &quot;Anglo-Saxon&quot; west Germanic tribes who migrated from Angeln and Lower Saxony in Germany and from Jutland (Denmark) to England via -- and who also settled -- the Frisian coastal regions of Holland and Germany. Frisian and English are closely related west Germanic languages that ordinary folk have found to be mutually intelligible.</i><br /><br />The British geneticist, Mark Thomas, made this same point 10 years ago in his research on the Y-chromosome. Nice to see genetic research backing up historical claims.<br /><br />http://mbe.oxfordjournals.org/content/19/7/1008.fullAverage Joehttps://www.blogger.com/profile/12203996329459638052noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-36781142174156530152012-01-12T17:54:19.927+02:002012-01-12T17:54:19.927+02:00For the large number of individual clusters, the r...For the large number of individual clusters, the results look plausible. Color me skeptical regarding the micro-clusters in places where populations that been stable so long that cryptic relatedness is a serious problem. <br /><br />I&#39;d be interested to see how the analysis would change if only one individual from each two or three person microcluster were included and the data were re-run (alternately, perhaps one could set a minimum cluster size of three or four).Andrew Oh-Willekehttps://www.blogger.com/profile/02537151821869153861noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-72027872538054759282012-01-12T12:24:13.572+02:002012-01-12T12:24:13.572+02:00I was particularly struck by how the English clust...<i>I was particularly struck by how the English cluster with the Dutch. In the fastIBD version all 12 English cluster with 5 of 9 Dutch, while 3 of the other 4 Dutch cluster with Germans and 1 with Norwegians and Swedes. By comparison, only 2 of 22 Irish cluster with the English; only 1 of 33 Cornish, none of the 4 Argyll (in western Scotland) and none of the Orcadian cluster with the English. In contrast the Russian_D, Polish and Ukrainian and other Slavs all cluster together even though they separated at the brink of recorded history.</i><br /><br />Neither the inclusion of different populations in a single cluster (as is the case for Slavs), nor the assignment of individuals from a single population to multiple clusters (as is the case for the Dutch) has a simple interpretation.<br /><br />In the latter case, it could be an artifact of the small size of Dutch_D. Clusters are formed when populations are distinctive relative to other included populations, and when they have enough individuals to make this distinction apparent.<br /><br />In the former case, differences between Slavs may emerge with e.g., higher sample sizes, or higher number of clusters (after all, Mclust chooses the number of clusters via BIC which balances fit with parsimony, so it&#39;s conservative), etc. <br /><br />It should also be noted that if two populations belong to the same cluster, this does not mean that there are no differences between them. Rather it means that in the context of the included populations there are no major &quot;gaps&quot; in the distribution of individuals.<br /><br />By sampling more individuals, one usually &quot;fills in the gaps&quot; of the genetic map: this has a detrimental effect on the ability to infer clusters. At the same time, one &quot;raises the peaks&quot; of the mountains of the genetic landscape. <br /><br />Clusters becomes apparent when the &quot;mountains&quot; of the genetic landscape (i.e. blobs of similar individuals) dominate the valleys of transitions between groups.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-79756435362559863322012-01-12T10:51:27.026+02:002012-01-12T10:51:27.026+02:00Thank you for your help Dienekes.
When i will have...Thank you for your help Dienekes.<br />When i will have money I will enjoy to your Project.<br />I am from a small town of southern Italy where people speak a strange kind of Greek. The region is calle Grecia Salentina. Do you know it!?bauhttps://www.blogger.com/profile/13358664543737897087noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-78229784408665432202012-01-12T07:45:34.308+02:002012-01-12T07:45:34.308+02:00I was particularly struck by how the English clust...I was particularly struck by how the English cluster with the Dutch. In the fastIBD version all 12 English cluster with 5 of 9 Dutch, while 3 of the other 4 Dutch cluster with Germans and 1 with Norwegians and Swedes. By comparison, only 2 of 22 Irish cluster with the English; only 1 of 33 Cornish, none of the 4 Argyll (in western Scotland) and none of the Orcadian cluster with the English. In contrast the Russian_D, Polish and Ukrainian and other Slavs all cluster together even though they separated at the brink of recorded history.<br /><br />That surely corroborates the traditional historical account that the English are descended from &quot;Anglo-Saxon&quot; west Germanic tribes who migrated from Angeln and Lower Saxony in Germany and from Jutland (Denmark) to England via -- and who also settled -- the Frisian coastal regions of Holland and Germany. Frisian and English are closely related west Germanic languages that ordinary folk have found to be mutually intelligible.<br /><br />Quote:<br /><br />http://en.wikipedia.org/wiki/Frisians<br /><br />&quot;<i>When conditions improved Frisia would receive an influx of new settlers, mostly Angles and Saxons, and these would eventually be referred to as &#39;Frisians&#39;, though they were not necessarily descended from the ancient Frisii. It is these &#39;new Frisians&#39; who are largely the ancestors of the medieval and modern Frisians.[9]</i>&quot;<br /><br />Researchers at UCL and some other geneticists have argued in favour of the same account.<br /><br />Quote:<br /><br />http://news.bbc.co.uk/1/hi/wales/2076470.stm<br /><br />&quot;<i>Academics at University College in London comparing a sample of men from the UK with those from an area of the Netherlands where the Anglo-Saxons are thought to have originated found the English subjects had genes that were almost identical. But there were clear differences between the genetic make-up of Welsh people studied.</i>&quot;<br /><br />* * *<br /><br />By the way, it is intriguing that the two Russian samples barely cluster at all! Different regions?apostateimpressionshttps://www.blogger.com/profile/08992369104954433139noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-22760410028658262752012-01-12T00:01:08.906+02:002012-01-12T00:01:08.906+02:00I don&#39;t see an easy way to do that, since this...I don&#39;t see an easy way to do that, since this is based on DNA segments, and a tool like that would almost certainly have to deploy such segments which would violate the no-distribution principle for participant data.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-14324243055516185552012-01-11T21:52:33.855+02:002012-01-11T21:52:33.855+02:00Dienekes,
Will you be releasing a utility based o...Dienekes,<br /><br />Will you be releasing a utility based on this, for non-participants - due to other family members already being participants - and/or mixed-ethnicity individuals?pconroyhttps://www.blogger.com/profile/10312469574812832771noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-86391284804033258742012-01-11T20:38:52.622+02:002012-01-11T20:38:52.622+02:00fastIBD outputs a list of segments together with t...fastIBD outputs a list of segments together with the probability that they are IBD. You can calculate the length of these segments in Morgans using recombination files, such as the following.<br /><br />http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/latest/rates/Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-7785493.post-39152559767334800622012-01-11T17:17:12.251+02:002012-01-11T17:17:12.251+02:00Nice,
I would like to try this analysis.
Is it the...Nice,<br />I would like to try this analysis.<br />Is it the code that calculates how much IBD sharing exists in a pair of inds available.<br /><br />I would be REALLY grateful if you could help me.<br /><br />THANK YOU.bauhttps://www.blogger.com/profile/13358664543737897087noreply@blogger.com